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In 2006, a capital campaign led to the creation of a sizeable endowment. Previously known as the Institute of International Economics, it changed its name that same year in recognition of Peter G. Peterson's role in the capital campaign and for his longstanding support of the Institute since the early 1980s.

The Institute's annual budget is about $12-13 million and it is financially supported by foundations, private corporations, and individuals, as well as earnings from its publications and capital fund.[5]

In an opinion piece for The New York Times published in 2016, Steven Rattner called the new building of the Peterson Institute "the locker room of the Team Globalization and Free Trade cheering squad." We should not close our borders or retreat from the world, said Rattner, but free trade has winners and losers, and "we need to be more sensitive to the losers and try to help," for example by redistribution of income through the tax system, which, he said, we haven't been doing. He goes on to state that Ross Perot was right when he said that the North American Free Trade Agreement would transfer American jobs to Mexico, particularly in manufacturing. From 2009 to 2013, employment in the American auto manufacturing sector rose by 23%, from 560,000 to 690,000. But employment in the Mexican auto sector rose from 368,000 to 589,000, or 60%. "I’m happy that 221,000 more Mexicans got jobs," he writes, "but let’s be honest: Absent open borders, many of those jobs would have been in America." He concludes by pointing out that wages in American auto manufacturing are down by 12.7%. Furthermore, American auto manufacturing compensation was $35.67 an hour; in Mexico, it was $6.36 an hour. Adam Posen, then the Peterson Institute's director, responded that “fetishization” of any industry was “immoral.”[7]